Can you point me to spark_genes and their README?

ngs-tools/tools/spark_genes/README.txt

Sorry - I thought you were referring to some other project with that name! Oops.

The genes.jar is created by the build. It is the output of the spark_genes script build.sh.

Please note also that this is not part of our production release. You are welcome to build it, but you will notice that it has rough edges such as rm *.class rather than rm -f *.class which causes complaints on first run or when there are missing dependencies.

Ok-so I have to execute build.sh in the directory as well, correct? That wasn't laid out in the docs so I didn't know I had to do that.

Yes, sorry for the confusion - this is not part of our actual release.

We have code in our repositories that does not get built. If we are releasing it and standing behind it, it gets built and installed. For some of the side or experimental projects, the code is there but does not get built by the main make. This is one of the reasons you caught me by surprise.

spark_genes does work, but you may have to poke around a bit to figure out how, or wait until Monday when its author is back in the office to comment.

Ok, sounds good, thanks!

I spoke with Ben Busby about a problem I was facing (I need count data from a bunch of NGS data) and he said this would be a great tool to use instead of downloading bam files so I'm trying to see how I can use the tool.

If there's more stable and documented versions let me know!

Thanks, will do. The same author just wrote a tool that performs the basic work necessary for variant calling directly from SRA, but it is still in (working) prototype shape and we have more work to do on it. It's pretty cool!

Yeah it all seems really useful, thanks for the help! I'll wait until the author can get back to me.